The article introduces MUMmer 3.0, an open-source software for comparing large genomes, which is significantly improved in terms of speed, memory usage, and functionality compared to its predecessors. MUMmer 3.0 addresses the need for efficient and versatile genome comparison tools, especially for closely related and distantly related species. Key improvements include a complete rewrite of the suffix-tree code, which reduces memory usage and enhances performance. The software now supports multi-contig queries and references, and includes new features such as non-unique maximal matches and amino acid-based alignments. Two new graphical viewers, DisplayMUMs and MapView, are also introduced to facilitate the analysis of genome alignments. The article provides several examples demonstrating the capabilities of MUMmer 3.0 in comparing genomes of different evolutionary distances, from closely related species like Drosophila melanogaster and Drosophila pseudoobscura to more distantly related species like Anopheles gambiae and Drosophila melanogaster. The authors conclude by highlighting the versatility and efficiency of MUMmer 3.0, emphasizing its potential for advancing research in genome comparison and assembly.The article introduces MUMmer 3.0, an open-source software for comparing large genomes, which is significantly improved in terms of speed, memory usage, and functionality compared to its predecessors. MUMmer 3.0 addresses the need for efficient and versatile genome comparison tools, especially for closely related and distantly related species. Key improvements include a complete rewrite of the suffix-tree code, which reduces memory usage and enhances performance. The software now supports multi-contig queries and references, and includes new features such as non-unique maximal matches and amino acid-based alignments. Two new graphical viewers, DisplayMUMs and MapView, are also introduced to facilitate the analysis of genome alignments. The article provides several examples demonstrating the capabilities of MUMmer 3.0 in comparing genomes of different evolutionary distances, from closely related species like Drosophila melanogaster and Drosophila pseudoobscura to more distantly related species like Anopheles gambiae and Drosophila melanogaster. The authors conclude by highlighting the versatility and efficiency of MUMmer 3.0, emphasizing its potential for advancing research in genome comparison and assembly.